Module 01

Module 01 portfolio check

Installation check
- Completion status:
- Comments:
Portfolio repo setup
- Completion status:
- Comments:
RMarkdown Pretty PDF Challenge
- Completion status:
- Comments:
Evidence worksheet_01
- Completion status:
- Comments:
Evidence worksheet_02
- Completion status:
- Comments:
Evidence worksheet_03
- Completion status:
- Comments:
Problem Set_01
- Completion status:
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Problem Set_02
- Completion status:
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Writing assessment_01
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Additional Readings
- Completion status:
- Comments

Data science Friday

Installation check

Screenshot_GIT

Screenshot_GitHub

Screenshot_Rstudio

Portfolio repo setup

cd ~/documents
mkdir MICB425_portfolio
touch ID.txt
git init git add .
git commit -m“first commit”
git remote add origin https://remote_repository_URL
git remote -v
git push -u origin master

RMarkdown pretty PDF challenge

R Markdown PDF Challenge

The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.

http://phdcomics.com/ Comic posted 1-17-2018

Challenge Goals

The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)

hint: go to the PhD Comics website to see if you can find the image above
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown

Here’s a header!

Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents)

Another header, now with maths

Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! ~~A calculator~~ R is here:

1231521+12341556280987

## [1] 1.234156e+13

Table Time

Or maybe, after you’ve added those numbers, you feel like it’s about time for a table!
I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the ^future.

library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")

I made this table with kable in the knitr package library
	speed	dist
	Min. : 4.0	Min. : 2.00
	1st Qu.:12.0	1st Qu.: 26.00
	Median :15.0	Median : 36.00
	Mean :15.4	Mean : 42.98
	3rd Qu.:19.0	3rd Qu.: 56.00
	Max. :25.0	Max. :120.00

And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!

Data science assignment 4

library(tidyverse)

## -- Attaching packages ---------------------------------------------------------------------- tidyverse 1.2.1 --

## v ggplot2 2.2.1     v purrr   0.2.4
## v tibble  1.4.2     v dplyr   0.7.4
## v tidyr   0.8.0     v stringr 1.2.0
## v readr   1.1.1     v forcats 0.2.0

## -- Conflicts ------------------------------------------------------------------------- tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()

source("https://bioconductor.org/biocLite.R")

## Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help

biocLite("phyloseq")

## BioC_mirror: https://bioconductor.org

## Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).

## Installing package(s) 'phyloseq'

## package 'phyloseq' successfully unpacked and MD5 sums checked
## 
## The downloaded binary packages are in
##  C:\Users\Lukas\AppData\Local\Temp\RtmpUNVGzp\downloaded_packages

## installation path not writeable, unable to update packages: MASS, mgcv,
##   nlme, rpart

library(phyloseq)

metadata = read.table(file="Saanich.metadata.txt", header = TRUE, row.names=1, sep= "\t", na.strings= c("NAN", "NA", "."))

OTU = read.table(file="Saanich.OTU.txt", header = TRUE, row.names=1, sep= "\t", na.strings= c("NAN", "NA", "."))

load("phyloseq_object.RData")

Exercise 1

ggplot(metadata, aes(x=NO3_uM, y=Depth_m)) +
  geom_point(shape=17, color = "purple")

Exercise 2

metadata %>% 
  select(matches("temp"))

##              Temperature_C
## SI072_S3_010        12.854
## SI072_S3_020        11.005
## SI072_S3_040         9.536
## SI072_S3_060         8.540
## SI072_S3_075         8.480
## SI072_S3_085         8.538
## SI072_S3_090         8.599
## SI072_S3_097         8.647
## SI072_S3_100         8.703
## SI072_S3_110         8.727
## SI072_S3_120         8.796
## SI072_S3_135         8.882
## SI072_S3_150         9.002
## SI072_S3_165         9.041
## SI072_S3_185         9.091
## SI072_S3_200         9.117

metadata2 = metadata %>%
  mutate(Temperature_F = Temperature_C *9/5 +32) 


metadata2 %>%
  select(Temperature_F)

##    Temperature_F
## 1        55.1372
## 2        51.8090
## 3        49.1648
## 4        47.3720
## 5        47.2640
## 6        47.3684
## 7        47.4782
## 8        47.5646
## 9        47.6654
## 10       47.7086
## 11       47.8328
## 12       47.9876
## 13       48.2036
## 14       48.2738
## 15       48.3638
## 16       48.4106

ggplot(metadata2, aes(x=Temperature_F, y=Depth_m)) +
  geom_point(shape=19, color = "purple")

Exercise 3

physeq_percent = transform_sample_counts(physeq, function(x) 100 * x/sum(x))
plot_bar(physeq_percent, fill="Domain") + 
  geom_bar(aes(fill=Domain), stat="identity") +
  labs(title="Domains from 10 to 200m in Saanich Inlet", x = "Sample depth", y = "Percent relative anbundance")

Exercise 4

faceted = gather(metadata, key = "Nutrient", value = "uM", NH4_uM, NO2_uM, NO3_uM, O2_uM, PO4_uM, SiO2_uM)

ggplot(faceted, aes(x=Depth_m, y=uM))+
  geom_line()+
  geom_point()+
  facet_wrap(~Nutrient, scales="free_y") +
  theme(legend.position="none")

Origins and Earth Systems

Evidence worksheet 01

Whitman et al 1998

Learning objectives

Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.

General questions

What were the main questions being asked?

The main questions were:
- To determine the number of prokaryotes in different habitats
- Which habitats are the most important ones; contribute the most to the abundance of microbes
- The amount of carbon stored in prokaryotes
- Amounts of other nutrients (N, P) in prokaryotes
- Turnover rates of the microbes in different habitats
- Which habitats are the most productive ones
- Estimate prokaryotic diversity (higher turnover leads to more mutations, diversity)

What were the primary methodological approaches used?

-Sampling of prokaryotes from different habitats, (top 200m of open ocean, ocean below 200m, different soils, subsurface in various dephts etc), quantification of cells in these samples.
-Estimation and extrapolation of cell abundances in habitats that could not be sampled.
-Research of data obtained from previous studies for estimations of cell abundance.
-Extrapolation, estimations, assumptions, mathematical formulas to calculate cell numbers, nutrient contents etc.
Examples of approaches:
-Open ocean: average cell density (cells/ml water), cell volume.-> estimate number of cells
-Subsurface: few samples taken, depth profile generated, extrapolation to 4km depth.
2nd approach: porosity of terrestrial surface 3%, 0.016% of pores occupied. -> use cell volume to calculate cell number
3rd: groundwater data for estimation
-Soil: estimations from direct cell counts from different soils

Summarize the main results or findings.

There are three habitats that mainly contribute to earth’s prokaryotic abundance:
-Open ocean (1.2x 10²⁹ cells)
-Soil (2.6x 10²⁹ cells)
-Subsurfaces ( terrestrial, below 8m and marine below 10cm) (0.25-2.5x 10³⁰ cells)

Further important habitats but with minor contributions to total cell number:
- Animals, Leaves, Air

->Total number of prokaryotes estimated to 4-6x 10³⁰ cells

Total prokaryotic carbon: 350-550 Pg (1Pg= 10^15 g)
-> 60-100% of total carbon of plants

Total prokaryotic nutrients (N,P) are circa 10 fold more than in plants. (N: 85-130 Pg, P: 9-14 Pg)

Turnover times in different habitats:
- Ocean above 200m: 6-25 days
- Ocean below 200m: 300 days
- Soil: 2.5 years
- Subsurface: 1-2x 10³ years (likely inaccurate, too high number, indicates that current understanding of subsurface prokaryotes is incomplete)

Ocean above 200m has highest cellular productivity, highest number of cells per time produced. (8.2*10^29 cells/year)
-> highest cellular productivity leads to most mutation events, diversity

Total cellular production rate on earth: 1.7x 10³⁰ cells per year

-> Large population size and turnover rates generate a huge potential for microbial diversity.-> leads to the opportunity of emergence of new cycles, pathways
-> Number of prokaryotic species may be greatly underestimated

Do new questions arise from the results?

The extremly long turnover rate for subsurface prokaryotes indicates that this habitat is not yet understood very well and needs to be further investigated

Determination of prokaryotic diversity:
- Huge prokaryotic populations with fast turnover rates (especially in open ocean) have the potential for a very large genetic diversity due to many mutation events. Prokaryotes have a much higher potential for simultaneous mutations than eukaryots and should therefore be differently treated in phylogenetic analyses. The number of prokaryotic species may be much higher than currently estimated through a DNA melting temperature method.
-> The diversity of prokaryotic species must be further investigated to understand the earths communities and its contribution to biogechemical processes.

-Paper is from 1980.-> How exact are the obtained numbers, estimations? Are there better technologies, more samples available to repeat calculations (especially for subsurface samples)?
-Has abundance and diversity of microbes changed since 1980?

Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

The assumptions and methods of the calculations were often not very well explained or completely absent. As most of the results in this paper are based on assumptions and estimations, it would have been useful if they were more transparent in their calculations. Therefore, also some more detailed discussion about the precision of the obtained numbers with error estimates or confidence intervals for example would have been usefull.

Problem set 01

Learning objectives:

Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.

Specific questions:

What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.

Open ocean: Total 1.2x 10²⁹ cells
-Top 200m: 3.6x 10²⁸
-Below 200m (incl. 10 cm of sediment): 8.2x 10²⁸

Soil: 2.6x 10²⁹ cells

Subsurfaces: ~3.8x 10³⁰ cells (uncertain, estimation)

What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?

Upper 200m: 3.6x 10²⁸ cells
->2.9x 10²⁷ autotrophs (cyanobacteria)
8.06% are autotrophs (cyanobacteria)

These 8% of autotrophic bacteria have to assimilate enough carbon to sustain the requirement of additional carbon from the 92% heterotrhopic cells.

This ratio means that 8% of assimilating autotrophs can sustain the need of additional carbon from outside the oceanic carbon cycle for the 92% of heterotrophes. Therefore, there is much more carbon cycling within the ocean than new carbon is fixed from the atmosphere to the ocean or that carbon is ‘lost’ from the ocean to the atmosphere.

What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?

Autotroph: CO2 as carbon source used. Fix inorganic carbon to biomass.
Heterotroph: not CO2 as carbon source.-> organic carbon needed.
Lithotroph: inorganic electron donor like NH3, H2S

Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?

4km below the surface. (4 km below terrestrial surface or marine sediments)
At 4km below surface, the temperature is about 125 degrees celsius, which is the temperature-limit for prokaryotes to live. In terrestrial habitat, temperature rises about 22 degrees celsius per km.

Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?

Up to 77km (But not really living cells up there, only transient state, spores…)
More realistic: 20km
Limiting factor: cold temperature (up to -90 degrees), radiation, low pressure, no nutrients
-> Mnt. Everest: 8.8km + 20km on top-> 28.8 km

Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?

Mariana trench: ~10.9 km deep, from this point, microbes can live up to 4km further down below marine sediment-surface.
-> from 20km on top of Mnt. Everest to 4km below Mariana trench -> total of 44 km

How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)

For annual cellular production, population size and growth rate must be taken into account.

-> Population size x Turnover rate (years)= Annual cellular production
->Ocean above 200m:
Pop size = 3.6x 10²⁸ cells
Turnover time in days: 16 -> Turnover rate = 365/16= 22.81 per year
-> 3.6x 10²⁸ Cells x 22.81 Turnovers per year = 8.2x 10²⁹ cells per year

->in soil:
pop. size= 2.6x 10²⁹ cells
Turnover rate = 0.4 per year (= 365/900)
-> 2.6x 10²⁹ x 0.4= 10²⁹ cells per year

What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?

Net productivity in ocean: 51 Pg/year
Prokaryotic carbon in ocean: 0.7-2.9 Pg
Carbon in one cell: 10 fg/Cell -> 20 x 10^-30 pg/cell
3.6*10²⁸ cells x 20x 10^-30 pg/cell= 0.72 Pg of carbon in marine heterotrophes
Carbon efficiency: 20%. But factor used in paper: 4 (!?)
4 x 0.72 Pg = 2.88 Pg/year
85% of net productivity consumed in upper 200m.-> 51Pg x 0.85= 43.35 Pg
43 pg/yr / 2.88 pg/yr = 14.9 Turnovers per year -> Turnover every 24.5 days.

85% of net productivity consumed in upper 200m.-> 51Pg x 0.85= 43.35 Pg

43.35 Pg / 0.7 Pg = 61 per year turnover rate max
43.35 Pg / 2.9 = 15 per year turnover rate min

-> the net productivity has to be four times (not 5?!) the amount of the carbon of prokariots to support their turnover.
- turnover rate can not exceed 15-60 per year.
Relationship varies because different fractions of the primary productivity reach different depths in different habitats. ( in soil, carbon gets burried much slower than carbon can sink in the ocean.- in ocean more carbon available when closer to the surface because more sunlight->more autotrophs present, more photosynthesis possible.

How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10^-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)

(4 x 10^-7 mutations per gene per generation)⁴ = 2.56 x 10^-26 mutation rate for 4 simoultanous mutations per gene per generation
3.6 x 10²⁸cells x 22.8 turnovers per year = 8.2 x 10²⁹ cells per year
8.2 x 10²⁹cells per year x 2.56 x 10^-26 mutations per generation = 2.1 x 10⁴ times per year => four simoultanous mutations every 0.4 hours.

Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?

Genetic diversity and adaptive potential might be much higher than previously expected. The number of prokaryotic species might be much higher than estimatad with DNA melting temperature method. The high diversity leads to the potential to adapt to changing environments and new metabolic pathways and cycles can emerge. Through the large number of prokaryotic cells and their high diversity, the microbes even have the potential to alter global nutrient cycles.

Microbes can not only diversify by point mutations, but also by bigger rearrangements in the genome (inversion, duplication, deletion etc). Else, genes (plasmids) could be transferred during conjugation, transformation or transduction, which allows fast adaptation through horizontal gene-transfer.

What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?

The enormous abundance of prokaryotes and the high turnover rates lead to a huge diversity. New mutations leading to new metabolic functions, pathways and cycles occur continously. Therefore, the metabolic potential is not only unimaginably high, but can also expand constantly to previously unknown emerging properties. Thus, microbes have the potential to significantly participate in and alter important biogeochemical cycles.

Evidence worksheet 02

Key events in the evolution of Earth systems

Hadean: 4.6 Ga: Formation of earth
4.5 Ga: Moon formed by impact of inner planet. Induced spin, tilt of Earth, leading to day/ night cyles and seasons.
4.4 Ga: Oldest zircoins, formation of Oceans, atmosphere 4.3-3.8 Ga: Heavy bombardment of Earth 4.1 Ga: First evidence for life: Carbon isotopes preserved
4.0 Ga: Plate subduction
- Oldest rock: acasta gneiss in Canada. -> Silica-rich rocks - water Oceans needed to provide cool, hydrated lithospheric plates to create rocks
- CO2 as greenhouse gas, CO2 rich ocean.-> reacts with basalt to form carbonates.-> CO2 decreases, atmosphere cools down-> surface temperature glacial -methane as greenhouse gas

Archaean: 3.8 Ga: Oldest sedimentary rocks,
Carbon isotopes: Evidence for life in sedimentary rocks in greenland Photosynthesis possible, Rubisco -Cyanobacteria 3.5 Ga: Evidence for photosynthesis in microfossils, stromatolites, fossil biofilms -rubisco -Sun weak, methane as greenhouse gas, warming shield
3 Ga: Glaciation because of oxygen production, less methanogen production.- less greenhouse effect
-Life on land: great oxydation event-> glaciation
-Large carbon isotope signals for carbon fixation -well developed stromatolites in ontario, south africa

2.7 Ga: -well developed stromatolites -direct evidence for life: molecular fossils of biological lipids from western australia. -hydrocarbon biomarkers characteristic of cyanobacteria imply oxygenic photosynthesis -Steranes as evidence for presence of eukaryotes

2.2 Ga: -Complex eukaryotes, oxygen level increased sharply -Change of anaerobic (microaerobic) air to oxic air leads to significant change of living biota.-> anaerobes go extinct.
-Cellular cybernetic switch between mitochondria, chloroplasts. - may control link between photosynthesis and N fixation.

Proterozoic:
-1.8 Ga: Eukaryotes, algae, symbiosis. - changing carbon cycle, several global glaciations.- snowball Earth -macroscopic life forms

-540 Ma: End of precambrian: cambrian explosion- emergence, diversification of animals. -expansion of mulitcellular evolution

phanerozoic: 400 Ma: devonian explosion: land plants, gigantism -strong increased oxygenation of atmosphere -Carboniferous period: fish, cephalopods, corals

300 Ma: Permian extinction (95% of species) -followed by rapid speciation, rise of dinosaurs -Formation of pangea, dry, harsh climate

-66 Ma: Cretaceous-tertiary extinction event - dramatic global warming -diversification of mammals, increasing size of mammals -dominating forest

23 Ma: neogene; Ice age

6 Ma: First hominins

2.6 Ma: Quaternary period

200’000 BP: Homo sapiens appears

Dominant physical/ chemical characteristics of Earth systems

4.6 Ga:
-High CO2 pressure; heat radiated to space -500 degrees Celsius
-CO2 tied up in carbonate minerals (limestone) -Ocean filled with water -Water as greenhouse gas, as vapour high in atmosphere, phtolysed into hydrogen and oxygen, hydrogen lost to space

4.5 - 4 Ga: -100 degrees Celsius
-Many meteorite impacts, heating up earth to >100 degrees. -> ocean vapourized -Seawater chemistry controlled by volcanism -Ice house, CO2 rising as greenhouse gas

3.8 Ga: -Meteorite bombardment halted.-> seawater chemistry stabilized -sulphur reduction -methanogenesis: greenhouse gas, heating up earth (Earth would have been glacial without methane shield because of weaker sun)

3.5 Ga: -Earth still anoxic -Hydrothermal, volcanogenic habitats -Microbes spread on coastal fringes, deeper water, deep hydrothermal vents

2.7 Ga: -well developed stromatolites

2.2 Ga: -oxygen level sharply increased.-> complex eukaryotes -Rocks recognized as red beds-> indicate oxidation -Change of anaerobic (microaerobic) air to oxic air leads to significant change of living biota.-> anaerobes go extinct.

Problem set 2

What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?

Geophysical processes: Plate tectonics and atmospheric photochemical processes. These two processes allow for the interaction of molecules and their cyclation.

Abiotic geochemical reactions are based on acid/base chemistry; proton transfers

Biogeochemical processes: Redox reactions driven mostly by microbes. -> Formation of two half-cells leads to linked cycles.

Biotic processes are based on redox reactions; electron transfers

Biogeochemical processes depend on resupply of C, S and P by tectonic cycles in geological time-scales. Abiotic cycles can supply biogeochemical reactions with new molecules carrying electrons which are required for the redox reactions. Therfore, abiotic acd/base reactions are interconnected with biotic redox reactions. Both reaction types support the other type with metabolites and energy required to sustain their cycles. This connection also leads to feedback on the microbial evolution, changing their metabolism and eventually the global redox state.

â¢ Why is Earthâs redox state considered an emergent property?

The Earth’s redox state depends on microbial metabolism which in turn adapts to the properties of geochemical cycles and therefore is subject to constant change. Further, a large part of the Earth’s redox state is determined by photosynthesis, which is a process independent of already available energy stored in metabolites. Thus, many different processes and cycles are nested in a complex manner and together lead to the Earth’s redox state as an emergent property.

â¢ How do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?

Reversible metabolic pathways can be directly related and catalyzed by microbes from similar species. On another scale, the reversible pathways may be catalyzed in a more global manner, by very diverse microbes. An expample for the first case is the formation of methane by methanogenic archaea, when the hydrogen pressure is high enough. In low hidrogen tension however, the reaction gets inversed by oxidation of methane to CO2. This reverse pathway is catalyzed by Archeae closely related to the methanogens. The second model can be represented by the global nitrogen cycle as an example. In this cycle, redox reactions are spatially and temporally separated and catalyzed by many different microbes. Atmospheric nitrogen is fixed by transformation of N2 to NH4+ by the oxygen sensitive enzyme nitrogenase. NH4+ is then oxidized in several steps to nitrite and finally nitrate in presence of oxygen. This nitrification is performed by several only distantly related bacteria and archaea. Again another set of microbes then uses the nitrate and nitrite as electron acceptors in anoxic conditions to generate energy. These bacteria thereby close this diverse, multipsecies cycle by the formation of N2.

Thermodynamic barriers to reversible electron flow can be overcome by coupling the unfavourable reaction to an energy yielding reaction such as catabolism of organic compounds. Else, reactions can be made thermodynamically favourable by changing the redox couples in a manner that again leads to a positive redox potential of the wanted reaction. Different microbes use the end products of other microbes as their substrate. In photosynthesis for example, CO2 is used as an electron acceptor to generate reduced organic carbon. In this reaction, H2O, which is used as electron donor, gets oxidized to O2 as end product. Different organisms can then ireverse these reactions by using the organic carbon as electron donor and O2 as electron acceptor.

â¢ Using information provided in the text, describe how the nitrogen cycle partitions between different redox ânichesâ and microbial groups. Is there a relationship between the nitrogen cycle and climate change?

In this cycle, redox reactions are spatially and temporally separated and catalyzed by many different microbes. Atmospheric nitrogen is fixed by transformation of N2 to NH4+ by the oxygen sensitive enzyme nitrogenase in bacteria like rhizobia. NH4+ is then oxidized in several steps to nitrite and finally nitrate in presence of oxygen. This nitrification is performed by several only distantly related nitrifying bacteria and archaea. Again another set of microbes then uses the nitrate and nitrite as electron acceptors in anoxic conditions to generate energy. These bacteria thereby close this diverse, multipsecies cycle by the formation of N2.

Humans strongly affect the global nitrogen cycle. Extensive usage of synthetic nitrogen fertilizers and fossil fuel processing lead to strong increases of reactive nitrogen in the atmosphere. These nitrogen species affect the abundance of the greenhouse gases CO2, CH4, O3 and N2O and therefore contribute to global warming.

â¢ What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?

The huge amount of microbial cells and their fast turnover leads to an enourmous genetic diversity through mutations. A further mechanism strongly promoting microbial diversity and evolution is horziontal gene flow. In different envrionments, different selective pressures exist, which require specialized metabolic pathways. Therefore, the high genetic diversity and many different strong selective pressures lead to a huge metabolic diversity of microbes. This huge diversity can be observed by the fact that to date, the number of new protein families discovered still rises linearly with the number of newly sequenced genomes. This means, the microbial and metabolic diversity are so high, that the total number of genes and protein families are still unknown and can only be estimated very imprecisely

â¢ On what basis do the authors consider microbes the guardians of metabolism?

The core genes responsible for most of the environment-specific metabolic pathways are spread in microbes all over the world. In addition, essential genes for general houskeeping pathways are highly conserved among global microbes.

Different environments favour the evolution and survival of the best adapted microbes. This means, less adapted microbes and their specialized pathways go extinct in a certain environment. However, thanks to the global distribution of the core gene set, the specialized metabolic pathways of this extinct strain are very likely to survive in another strain in a different environment. In addition, the survival of the essential genes is even more expected, as these genes are conserved throughout most of the microbes on earth. Thus, despite changing environments and the selective pressures they cause, the genes responsible for different metabolic pathways always survive in some micrboes which therefore can be considered as the guradians of metabolism.

Evidence Worksheet 03

Evaluate human impacts on the ecology and biogeochemistry of Earth systems

â¢ What were the main questions being asked?

Whether humans changed the Earth system strong enough that the stratighrapic signature is altered in a way that the current epoch can be considered as distinct from the Holocene.

To determine the time-point this human made stratigraphical signal became recognizable in a significant manner.

In general: To rieview anthropogenic markers of changes in different systems ( biochemical cycles, sediment composition, sea-level, climate, biotic systems)

â¢ What were the primary methodological approaches used?

The paper is a review. -> Results collected from other studies. Measured concentrations of different molecules, isotope frequencies, temperatures etc from different places (soil, ocean, glacier etc). -> Other measurements also taken to reconstruct/ extrapolate/ estimate the corresponding values of past times in Earth’s history. -> Comparison of values from present and past times to infer whether humans have caused a significant change in stratighrapic signature

â¢ Summarize the main results or findings.

anthropogenic deposits: (great acceleration at ~1950 CE) - products of mining, waste desposal, construction, urbanization. ( - great expansion of new minerals: new geological materials with long term persistance (new “rocks”) - Aluminium, concrete, organic polymers: “technofossils”, provide stratigraphic resolution in time scales of years to decades. -combustion of fossil fuels lead to global distribution of airborn particles: black carbon, inorganic ash spheres, sperical carbonaceous particles. These particles are long time persistent stratigraphic markers.

Modification of sedimentary processes: - Transformation of >50% of Earth’s land surface: landfills, urban structure, mine tailings, deforestation, cultivated soils, sediment retention (dams, leading to reduced flux, subsided deltas) - Ocean: coastal reclamation works, sediment reworking, sand extraction, rising sea level, eutrophication, coral bleaching -Subsurface: mineral extraction, waste storage

Geochemical signatures in sediments and ice: - Elevated concentrations of polyaromatic hydrocarbons, polychlorinated biphenyls, pesticide residues, lead, - Fertilizer usage: doubled concentrations of nitrogen and phosphorus in soil. Influx to lakes led to oxygen deficiency, increased animal mortality. - Decrease of ¹⁵N in lakes, ice sheet. - Increase in nitrate: values higher than any for the previous 100’000 years.-> distinct from Holocene background level. - Industrial metals: cadmium, chromium, copper, mercury, nickel, lead, zinc

Radiogenic signatures: - fallout from nuclear weapons testing: most widespread, globally synchronous anthropogenic signal. -> Start of Anthropocene may be defined by detonation of the trinity atomic device at alamogordo, 1945. - Increased ¹⁴C, ²³⁹P ( ²³⁹P may be best radioisotope for marking the start of the Anthropocene because of long half-life and low solubility)

Carbon cycle: - Atmospheric CO2: >400 ppm, exceeding Holocene levels since 1850 CE - ¹³C levels decrease of > 0.2% because burning of fossil fuels leads to increase of ¹²C (organic carbon has increased ¹²C because lighter isotope reacts faster in biochemical reactions (photosynthesis) - permanent signal, stored in tree rings, lime-stones, fossils -Increase of methane to 1700 ppb, 900ppb higher than highest value in past 800’000 years

Climate and sea-level change - Given orbital trend, earth should be cooling ( as it was since 8200 B.P. untill 1800CE) - emission of greenhouse gases lead to climate warming - Average temperature increase of 06.-0.9 degrees from 1906 to 2005, exceeding natural variability - Average global sea levels are higher than highest levels of the past 115’000 years. - rise of 3.2 mm per year from 1993 to 2010 - climate and sea-level changes are not as strong as other stratiraphic changes, but are likely to exceed the envelope of quaternary system baseline conditions. -change in planetary energy balance: radiative forcing increased by 2.29 Wm^-2 compared to 1750 CE. 8because of burning of fossil fuels)

Biotic change: - Extinction rates since 1500 CE are far above mean per-million-year background rates. - species abundances and assamblages strongly altered; transglobal species invasions, agriculture, fishing.

conclusion: - stratigraphic signatures are either novel or outside the range of variation of the holocene, supporting the formalization of the Anthropocene as stratigraphic epoch. - dating of begining of Anthropocene proposed to lay between 1945 and 1964 CE

â¢ Do new questions arise from the results?

Should the Anthropocene be formalized as epoch or left as informal time term?
How to define the Anthropocene. -> By GSSA (calendar age) or GSSP ( reference point in a stratal section) -> Define start point of the Anthorpocene (1945-1964)? -How are the stratigraphical changes going to proceed in the future? -> Make projections of climate, sea-level, biodiversity etc to future

â¢ Were there any specific challenges or advantages in understanding the paper (e.g. did the authors provide sufficient background information to understand experimental logic, were methods explained adequately, were any specific assumptions made, were conclusions justified based on the evidence, were the figures or tables useful and easy to understand)?

The Review mostly showed very well, on what data/assumptions/estimations their results are based. However, sometimes it was not clear, how the data were optained, i.e. which methods lead to the obtained results. Further, it is not always clear, how exact the obtained values for concentrations/ temperatures etc are. Especially for the estimations of the values for earlier points in time, some more information about error rates would have been useful.

Module 1 assay

“Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.”

Ever since the emergence of humans, we have been interacting with microbes. We live in symbiosis with microbes in many different aspects, which rises the important question whether we could survive without them. Microbial life emerged about 4.1 billion years before the first humans developed, which proofs that microbes can easily live without us. In contrast, confirming that humans cannot survive without the global catalysis provided by microbes, is much more challenging. Several aspects need to be considered in order to answer the question whether humans rely on the presence of microbes. Firstly, after their emergence, the microbes rapidly spread all over the earth and rose to incredible numbers of individuals. Secondly, fast reproduction and constant turnover of the cells leads to massive requirements of nutrients and thereby promotes the global turnover of these nutrients. The fast reproduction of microbes further generates an enormous genetic diversity through mutations, which allows the microbes to constantly adapt present pathways or even generate new metabolic processes. Through this extremely high abundance and diversity, microbes developed a massive potential not only to actively participate in, but also to significantly alter important biogeochemical cycles, which can be shown by several examples covered in this assay. Lastly, this potential for global catalysis leads to important, microbially driven environmental transformations on Earth, creating an inhabitable atmosphere. This not only allowed for the emergence of more complex organisms and the human species, but will also be important for human survival in the future.

Microbes have a massive potential to impact global cycles because of their sheer number of cells present. They account for by far the biggest part of the number of organisms alive on earth and arguably also the greatest part of nutrients stored in living beings. The number of prokaryotes living on earth could be obtained by cell counts of probes sampled from several different habitats. Subsequent projection and extrapolation for habitats not available for sampling led to an estimation of 4-6*1030 cells present (Whitman, Coleman, and Wiebe 1998). Considering average values of nutrient contents per cell, leads to the conclusion that microbes totally contain 60-100% of the amount of carbon stored in plants. The fraction of nitrogen and phosphorus stored in microbes is even higher, with about ten times more of these elements stored in microbes than in plants. These numbers show, that through their enormous abundance and capacity, microbes technically have the potential to provide important global catalysis.

In addition to the huge number of microbial cells, their fast turnover rates generate an even higher potential of the microbes to significantly catalyze and transform global cycles. An average turnover rate of 22 turnovers per year leads to about 8.2*1029 heterotrophic cells produced every year, just in the upper 200 meters of the ocean. Therefore, the vast amounts of cells continuously being produced further explains their impact on global cycles as their constant metabolism leads to massive requirements and turnover of nutrients. The constant turnover of prokaryotes additionally offers the opportunity to generate an enormous genetic diversity through billions of mutation events. The large genetic variation leading to continuous adaptation through evolution enables the bacteria to constantly generate new metabolic pathways and cycles. In summary, the fast microbial reproduction accounts for high nutrient requirement, global circulation of these nutrients and generation of metabolic diversity through evolving cells. This allows for the conclusion, that microbes have the potential to significantly transform the environment and even catalyze global cycles in such a powerful way that humans become dependent on their presence on Earth.

The enormous abundance, turnover and diversity provides a huge potential for the microbes to actively contribute to the composition of Earthâs properties. These contributions thereby are of such importance that humans would not be able to survive without microbes providing them, which can be shown by several examples. Firstly, marine microorganisms are responsible for the generation of nearly all of the oxygen present in the atmosphere (Kasting and Siefert 2002). The oxygen produced by plants only contributes to a small fraction of atmospheric oxygen because most of the O2 produced by plants is used up again by their own respiratory processes and upon decay of dead plant material. Therefore, the oxygen produced by microbes is substantial for human respiration and hence, also existence. Second, Earthâs redox state depends mostly on microbial life and therefore is an emergent property of their existence (Falkowski, Fenchel, and Delong 2008). This means, the global fluxes of some of the most important elements (H, C, N, O, S) are controlled in large parts by redox reactions which are catalyzed by prokaryotes. Thus, microbial photosynthesis not only provides humans with breathable air, but also drives the Earthâs oxidation in general, and finally, supplies heterotrophic organisms with reduced carbon. Further, not only photosynthesis, but many other microbial processes contribute to important global nutrient cycles. One example for a cycle largely controlled by microbes is the nitrogen cycle. Microbes catalyze all the steps present in the global nitrogen cycle and thereby control the oxidation state in which the nitrogen species are present in Earthâs atmosphere, soil and oceans. Many other prokaryotes and eukaryotes, that cannot process atmospheric nitrogen, rely on the supply of these nitrogen species provided by nitrogen-fixing microbes. Also humans rely on fixed nitrogen, which initially is provided by microbes and wanders through the food chain until eventually taken up as part of the human nourishment. All of these examples show, that the global nutrient cycles which are in large parts controlled by microbes, are of such importance, that human existence relies on their catalysis provided by microbes.

The potential of microbes to catalyze global processes does not only affect nutrient cycles, but also the global environment and climate. Microorganisms can significantly change the climate by altering the atmospheric composition. The production of several gases like methane and nitrous oxide strongly influences the global climate through the greenhouse effect. The great importance of this effect for the survival of organisms can be shown not only for present days, but also for early stages in time. In the distant past, about 3.5 billion of years ago, microbial methane production might have contributed to a global shield, warming up the planet (Nisbet and Sleep 2001). At this time, the sun was much weaker than today and therefore, without a greenhouse gas like methane, Earth would have been completely frozen over. By keeping the earth from freezing, this methane shield might have allowed for fast reproduction, leading to evolution and the emergence of more complex life-forms. About 500 million years later, microbes again significantly transformed the environment. The emergence of photosynthetic cyanobacteria led to a strong increase of the oxygen level in the atmosphere. This resulted in decreased viability of methanogenic organisms and therefore decreased methane concentrations, which in turn reduced the greenhouse effect. The consequence was a global glaciation, again significantly changing the composition of organisms capable of living on Earth. In summary, in the absence of microbes, the global environment with its properties as present now, could not have been created. In a world depleted of the global catalysis provided by microbes, Earthâs environment would have been very unfavorable for the emergence of complex life forms as they are present today. As the past times show, a stable environment, which can be provided and maintained by microbes, will also be necessary for humans to live in future times. If humans wanted to survive without microbes, they would have to artificially control all the cycles currently run by microbes. This, however, is most likely not possible. Humans will not be able to replace all the microbially driven cycles in an efficient way. We are not able to generate machines catalyzing processes as efficient as microbes do after millions of years of evolution. Further, as microbial diversity is unimaginably high, the range of the processes they catalyze can always adapt quickly to changing conditions. Humans will not be able to adapt their engineered machines fast enough in order to provide sufficient flexibility to changing demands.

In summary, the enormous number of prokaryotic cells present, their fast turnover and the high genetic diversity offer an unimaginable potential for the microbes to significantly contribute to the presence and properties of biogeochemical cycles. Microbes provide a global environment-composition which allowed for the emergence of humans and will also in the future be necessary for our persistence. From the beginning of our existence, we have been living in symbiosis with microbes. We do not only interact with microbes living in and on our bodies, but also with the global biogeochemical cycles they are a significant part of. Artificially replacing all of the processes provided by microbes will not be possible in a sufficient way. Therefore, existence of human life without the presence of microbes is most likely not possible as our survival strongly depends on stable global cycles, kept intact by microbes. Microbes have been the guardians of global metabolism for billions of years(Waters et al. 2016). It is very unlikely that humans could further exist without microbes present, continuously guarding global metabolic processes. A new question that arises is however, how likely it is, that the human race eventually manages to destroy this essential function of the microbes as guardians of global metabolism.

References

Falkowski, P. G., T. Fenchel, and E. F. Delong. 2008. ‘The microbial engines that drive Earth’s biogeochemical cycles’, Science, 320: 1034-9.

Kasting, J. F., and J. L. Siefert. 2002. ‘Life and the evolution of Earth’s atmosphere’, Science, 296: 1066-8.

Nisbet, E. G., and N. H. Sleep. 2001. ‘The habitat and nature of early life’, Nature, 409: 1083.

Waters, Colin N., Jan Zalasiewicz, Colin Summerhayes, Anthony D. Barnosky, ClÃ©ment Poirier, Agnieszka GaÅuszka,
Alejandro Cearreta, Matt Edgeworth, Erle C. Ellis, Michael Ellis, Catherine Jeandel, Reinhold Leinfelder, J. R. McNeill, Daniel deB. Richter, Will Steffen, James Syvitski, Davor Vidas, Michael Wagreich, Mark Williams, An Zhisheng, Jacques Grinevald, Eric Odada, Naomi Oreskes, and Alexander P. Wolfe. 2016. ‘The Anthropocene is functionally and stratigraphically distinct from the Holocene’, Science, 351.

Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. ‘Prokaryotes: the unseen majority’, Proc Natl Acad Sci U S A, 95: 6578-83.

Module 01 references

Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578â“6583. PMC33863 Falkowski, P. G., T. Fenchel, and E. F. Delong. 2008. ‘The microbial engines that drive Earth’s biogeochemical cycles’, Science, 320: 1034-9.